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annotate fasta_clipping_histogram.xml @ 2:9db07fd39f85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:53:35 -0400
parents f666895cbebd
children 8889eb864cef
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1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.1">
1
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2 <description>chart</description>
2
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.49">perl-gdgraph</requirement>
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 fasta_clipping_histogram.pl
9db07fd39f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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11 '$input'
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12 '$outfile'
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13 ]]></command>
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15 <inputs>
2
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16 <expand macro="fasta_input" />
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17 </inputs>
0
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18
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19 <outputs>
2
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20 <data name="outfile" format="png" metadata_source="input" />
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21 </outputs>
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22 <tests>
2
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23 <test>
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24 <param name="input" value="fasta_clipping_histogram-in1.fa" />
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25 <output name="outfile" file="fasta_clipping_histogram-out1.png" compare="sim_size" delta="512" />
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26 </test>
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27 <test>
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28 <param name="input" value="fasta_clipping_histogram-in2.fa" />
9db07fd39f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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29 <output name="outfile" file="fasta_clipping_histogram-out2.png" compare="sim_size" delta="512" />
9db07fd39f85 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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30 </test>
1
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31 </tests>
2
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32 <help><![CDATA[
0
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33 **What it does**
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34
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35 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
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36
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37 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
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38
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39 -----
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40
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41 **Output Examples**
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42
1
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43 In the following library, most sequences are 24-mers to 27-mers.
0
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44 This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
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45
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46 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
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47
1
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48 In the following library, most sequences are 19,22 or 23-mers.
0
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49 This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
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50
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51 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
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52
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53 -----
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54
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55 **Input Formats**
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56
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57 This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
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58
2
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59 >sequence1
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60 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
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61 >sequence2
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62 GTGTGTGTGGGAAGTTGACACAGTA
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63 >sequence3
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64 CCTTGAGATTAACGCTAATCAAGTAAAC
0
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65
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66 If the sequences span over multiple lines::
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67
2
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68 >sequence1
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69 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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70 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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71 aactggtctttacctTTAAGTTG
0
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72
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73 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
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74
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75 >sequence1
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76 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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77
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78 -----
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79
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80 **Multiplicity counts (a.k.a reads-count)**
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81
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82 If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
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83
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84 Example 1 - The following FASTA file *does not* have multiplicity counts::
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85
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86 >seq1
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87 GGATCC
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88 >seq2
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89 GGTCATGGGTTTAAA
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90 >seq3
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91 GGGATATATCCCCACACACACACAC
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92
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93 Each sequence is counts as one, to produce the following chart:
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94
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95 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
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96
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97 Example 2 - The following FASTA file have multiplicity counts::
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98
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99 >seq1-2
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100 GGATCC
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101 >seq2-10
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102 GGTCATGGGTTTAAA
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103 >seq3-3
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104 GGGATATATCCCCACACACACACAC
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105
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106 The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
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107
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108 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png
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109
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110 Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
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111
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112 ------
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113
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114 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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115
2
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116 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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117 ]]></help>
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118 <expand macro="citations" />
1
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119 </tool>